added mantel command

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 26cdcda0178bcfdbfc8c89fbbbced8866edb796c..f47427d62c2cc7f03615149b11cbfdee5135b083 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -10,16 +10,6 @@
 #include "corraxescommand.h"
 #include "sharedutilities.h"
 
-//********************************************************************************************************************
-//sorts highest to lowest
-inline bool compareSpearman(spearmanRank left, spearmanRank right){
-       return (left.score > right.score);      
-} 
-//********************************************************************************************************************
-//sorts lowest to highest
-inline bool compareSpearmanReverse(spearmanRank left, spearmanRank right){
-       return (left.score < right.score);      
-} 
 //**********************************************************************************************************************
 vector<string> CorrAxesCommand::getValidParameters(){  
        try {
@@ -47,8 +37,7 @@ vector<string> CorrAxesCommand::getRequiredParameters(){
 //**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(){    
        try {
-               abort = true;
-               //initialize outputTypes
+               abort = true; calledHelp = true; 
                vector<string> tempOutNames;
                outputTypes["corr.axes"] = tempOutNames;
        }
@@ -72,11 +61,11 @@ vector<string> CorrAxesCommand::getRequiredFiles(){
 //**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(string option)  {
        try {
-               abort = false;
+               abort = false; calledHelp = false;   
                globaldata = GlobalData::getInstance();
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
                
                else {
                        //valid paramters for this command
@@ -221,7 +210,7 @@ CorrAxesCommand::~CorrAxesCommand(){}
 int CorrAxesCommand::execute(){
        try {
                
-               if (abort == true) { return 0; }
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
                
                /*************************************************************************************/
                // use smart distancing to get right sharedRabund and convert to relabund if needed  //
@@ -656,7 +645,7 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                                        int numWithLowerRank = 0;
                                        float thisrank = otus[l].score;
                                        
-                                       for (int u = l; u < scores[j].size(); u++) {
+                                       for (int u = l+1; u < scores[j].size(); u++) {
                                                if (otus[u].score > thisrank) { numWithHigherRank++; }
                                                else if (otus[u].score < thisrank) { numWithLowerRank++; }
                                                count++;
@@ -666,9 +655,6 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                                        numDisCoor += numWithLowerRank;
                                }
                                
-                               //comparing to yourself
-                               count -= lookupFloat.size();
-                               
                                double p = (numCoor - numDisCoor) / (float) count;
 
                                out << '\t' << p;